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https://github.com/lilyminium/improper_orders
Which atom is central in your improper torsion?
https://github.com/lilyminium/improper_orders
Last synced: about 1 month ago
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Which atom is central in your improper torsion?
- Host: GitHub
- URL: https://github.com/lilyminium/improper_orders
- Owner: lilyminium
- License: mit
- Created: 2022-01-08T04:45:00.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-04-18T21:59:31.000Z (9 months ago)
- Last Synced: 2024-10-16T11:57:45.374Z (3 months ago)
- Size: 6.84 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Which atom is central in your improper torsion?
The central atom is indexed from 1, i.e. 3 indicates the third atom.
| Package | Improper type | Central atom | Links and notes |
|------------|---------------------|--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|
| AMBER | Periodic | 3 (or 2) | Torsions can be reversed for 1-4 torsions. https://github.com/MDAnalysis/mdanalysis/issues/2386 https://github.com/openmm/openmm/issues/220#issue-22877306 |
| ParmEd | Periodic | 3 | https://github.com/MDAnalysis/mdanalysis/issues/2386 |
| ParmEd | Harmonic | 1 | https://github.com/MDAnalysis/mdanalysis/issues/2386 |
| Gromacs | Periodic | 1 | https://github.com/MDAnalysis/mdanalysis/issues/2386 |
| Gromacs | Harmonic | 1 | https://github.com/MDAnalysis/mdanalysis/issues/2386 |
| OpenFF | Smirnoff (periodic) | 2 | https://github.com/openforcefield/openff-toolkit/issues/746#issuecomment-710574144 |
| OpenFF | Amber | 3 | https://github.com/openforcefield/openff-toolkit/issues/746#issuecomment-710574144 |
| CHARMM | all? | 1 | https://github.com/michellab/Sire/issues/193#issue-303038454 |
| MDAnalysis | all | any | MDAnalysis does not check connectivity. (However, calculating values of improper torsions assumes the central atom is first.) |
| NAMD | all? | 1 | Follows CHARMM |
| OpenMM | all | 1 | http://docs.openmm.org/7.2.0/userguide/application.html#periodictorsionforce |